You know, reading the text and seeing the thumbnail, it looks like the tree grew arms and is attempting to chase Juni. I was worried for more than a graphical bug there for a second.
Anyway, I find more ones:
x1004 y998
Future of Gaia might be bright, but not bugless:
x998 y1036
x1005 y1037
x1017 y1037
x1016 y1037
x1009 y1037 This one is at the same place in past.
x1013 y1037
I know I am looking like the biggest nitpicker now, but there is one more thing that annoys me a little: Underwater tube.
Aren't you planning to make some tileset with corners for it ?
Also, one part of tube is covered with waterfalls, others are not.
And one more thing - traveling via that tube is horribly boring. Maybe you should add some underwater plants and other stuff.
Edit:Some invisible layer 3 stuff at x1008 y1037.
Edit:One more from future at x1020y1038.
Some weird stuff grows at camel farm at x1056y1005.